Yeah, the Enclave parts in Fallout 2 do come across as a bit nonsensical. I think the reason why is that the devs were rushed for time. The producers were putting huge amounts of pressure on the devs for time, and they had focused lots of there efforts on earlier parts of the game like New Reno and Vault City, meaning that most endgame areas come across as kind of rushed.
Anyway, this is mostly lots of headcanoning ahead.
Yet, you can show up to the gas station with a suspicious car and claim to have hired an escort. That makes no sense whatsoever. Any recruits to the Navarro base would obviously come from the oil rig via verti birds.
IIRC, the Enclave does actively mention other bases across the continent in several parts of the game. That being said, The Oil Rig is always presented as there main base of operations. Maybe they are also accepting recruits from another base somewhere else in the continent, which maybe didn't have Vertibirds(Given that, as Matthew stated, they are relatively new technology)
As for the tanker...it makes no sense that they would park it at San Francisco. They would obviously park it somewhere where nobody other than enclave personnel could get to it in the first place (like, a deserted island or just in the middle of the ocean).
They had the FOB.
As far as they are concerned, nobody other than Enclave Personnel could get in anyway.
Also, the tanker ran on Diesel Fuel. They wouldn't want to waste precious oil in moving some old tanker they didn't care about away.
And somehow, nobody on the oil rig notices the tanker sailing up to it at all.
The defences on the Oil Rig are automated. If it registered the Tanker as a threat, it would have destroyed it.
The folks onboard probably noticed, but were too occupied by there project(Which was nearly done by the time The Chosen One entered the Oil Rig), they probably didn't care.
"thanks for giving me the code, now you must die" - Colonel Autist
"SANTIAGO!"
Well in a way that's one of the few things that makes sense. He knows the Lone Wanderer can still be a threat and they aren't needed anymore, so why not pop 'em?
Maybe he could have checked the codes worked first?
Also, he only shoots you if you give him the real codes, not if you lie. Unless he's a psychic, he shouldn't know the difference.
Truth is, the game wrote itself in to a hole where the plot would fall apart if a certain possibility happened. It's the same reason why The Chosen One dies if he loses the duel to Cameron in the Temple of Trials, because the entire game would fall apart if it continued to explore that possibility.